http://genome.sph.umich.edu/w/index.php?title=Template:SeqShopExtSetup&feed=atom&action=historyTemplate:SeqShopExtSetup - Revision history2024-03-28T19:11:05ZRevision history for this page on the wikiMediaWiki 1.35.9http://genome.sph.umich.edu/w/index.php?title=Template:SeqShopExtSetup&diff=14612&oldid=prevPpwhite: /* Download the Workshop Example Data */2017-02-02T15:09:55Z<p><span dir="auto"><span class="autocomment">Download the Workshop Example Data</span></span></p>
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</table>Ppwhitehttp://genome.sph.umich.edu/w/index.php?title=Template:SeqShopExtSetup&diff=11138&oldid=prevMktrost: Created page with "== Setup when running on your own outside of the SeqShop Workshop == ''This section is specifically for running on your own outside of the SeqShop Workshop.'' <div class="mw-c..."2014-07-03T20:15:12Z<p>Created page with "== Setup when running on your own outside of the SeqShop Workshop == ''This section is specifically for running on your own outside of the SeqShop Workshop.'' <div class="mw-c..."</p>
<p><b>New page</b></p><div>== Setup when running on your own outside of the SeqShop Workshop ==<br />
''This section is specifically for running on your own outside of the SeqShop Workshop.''<br />
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''If you are running during the SeqShop Workshop, please skip this section.''<br />
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<br />
=== Workshop Setup Steps ===<br />
'''If this is your first SeqShop tutorial, you need to run some initial setup steps.'''<br />
<br />
''These setup steps only need to be run once.''<br />
<div class="mw-collapsible" style="width:700px"><br />
If you have already run another SeqShop tutorial, you can skip these steps (select 'Collapse' to hide the steps that you can skip)<br />
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==== Download & Build GotCloud ====<br />
* cd to where you want GotCloud installed (you can change this to any directory you want)<br />
mkdir -p ~/seqshop<br />
cd ~/seqshop/<br />
* download, decompress, and build the version of gotcloud that was tested with this tutorial:<br />
wget https://github.com/statgen/gotcloud/archive/gotcloud.workshop.tar.gz<br />
tar xvf gotcloud.workshop.tar.gz<br />
mv gotcloud-gotcloud.workshop gotcloud<br />
cd gotcloud/src<br />
make<br />
cd ../..<br />
<br />
Remember the path to gotcloud/ - you will need to set the GC variable to the path.<br />
<br />
<br />
==== Download the Workshop Example Data ====<br />
wget http://www.sph.umich.edu/csg/mktrost/seqshopExample.tar.gz<br />
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=== Setup your run environment ===<br />
<br />
Environment variables will be used throughout the tutorial.<br />
<br />
We recommend that you setup these variables so you won't have to modify every command in the tutorial.<br />
<br />
<br />
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I'm using bash (replace the paths below with the appropriate paths):<br />
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* Point to where you installed GotCloud<br />
*:<pre>export GC=~/seqshop/gotcloud</pre><br />
* Point to where you installed the seqshop files<br />
*:<pre>export SS=~/seqshop/example</pre><br />
* Point to where you want the output to go<br />
*:<pre>export OUT=~/seqshop/output</pre><br />
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I'm using tcsh (replace the paths below with the appropriate paths):<br />
<div class="mw-collapsible-content"><br />
* Point to where you installed GotCloud<br />
*:<pre>setenv GC ~/seqshop/gotcloud</pre><br />
* Point to where you installed the seqshop files<br />
*:<pre>setenv SS ~/seqshop/example</pre><br />
* Point to where you want the output to go<br />
*:<pre>setenv OUT ~/seqshop/output</pre><br />
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</div></div>Mktrost